Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_057508804.1 ABB28_RS11700 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_001431535.1:WP_057508804.1 Length = 454 Score = 197 bits (501), Expect = 6e-55 Identities = 147/454 (32%), Positives = 230/454 (50%), Gaps = 28/454 (6%) Query: 3 KLFGTFGVRG-IANEEITPEFALKIGMAFGTLLKRE----GRERPLVVVGRDTRVSGEML 57 + FGT G+RG + I+ +F L++G AFG +L + GR RP+VV+G+DTR+SG M Sbjct: 5 RYFGTDGIRGRVGQGVISADFVLRLGNAFGRVLVAQQAAAGR-RPIVVIGKDTRISGYMF 63 Query: 58 KDALISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNG 117 + AL +GL++ G DV +G PTPA+ + T AD G VI+ASHNP NGIK G Sbjct: 64 EAALEAGLVAAGVDVQLLGPMPTPAVAFLTRTLGADAGIVISASHNPHYDNGIKFFSAQG 123 Query: 118 MGLKKEREAIVEELFFSEDFHRAKWNEIGE-LRKEDIIKPYIEAIKNRV----DVEAIKK 172 L E + E E F A+ ++G+ +R + I YIE K V D+ ++ Sbjct: 124 EKLDDATE-LALEAGIDEPFTTAESEKLGKAMRAREAIGRYIEFCKASVPRNFDLRGVR- 181 Query: 173 RRPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVK 232 +V+D ++GA P L RELG +V+++ A PDG N ++ V+ Sbjct: 182 ----LVLDCAHGATYHIAPLLFRELGAEVIAIGAAPDG--VNINAGVGSTHIDNLAAKVR 235 Query: 233 ALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG--GGLLVTTIATSNL 290 GAD G+A DGD DR + D+ G + GD ++A A + NG G +V T+ T+ Sbjct: 236 ETGADLGIAFDGDGDRVLMADDQGNPVDGDDLLFILARA-WQANGRLRGPVVGTLMTNFG 294 Query: 291 LDDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIV 350 L+ ++ +R+ VGD V +AL+E G +GGE +G ++ D D ++ +++ Sbjct: 295 LEQALEKLQIPFLRSNVGDRYVHQALVEGGGVLGGEASGHLLCLDRATTGDAIVSALQVL 354 Query: 351 EIFAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKII 410 +SG+ E + L + Q KT G+ A A ++ + + Sbjct: 355 VELRRSGQSLREALQPLSRVPQ-KTVNVRLGNVSAKATVQAASVQQA-----LVQAQQAV 408 Query: 411 FDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLE 444 G +R SGTEP++R+ EA +E L+ Sbjct: 409 AGRGRAFLRPSGTEPVVRVTVEADEATLMQETLD 442 Lambda K H 0.317 0.139 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 484 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 456 Length of database: 454 Length adjustment: 33 Effective length of query: 423 Effective length of database: 421 Effective search space: 178083 Effective search space used: 178083 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory